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Zr/Nb nanoscale multilayer coatings (NMCs) were studied after hydrogenation in a gaseous environment at 400 °C. The hydrogen distribution and content were determined by pressure and hydrogenation time. Increasing the pressure from 0.2 to 2 MPa resulted in different hydrogen distribution within the Zr/Nb NMCs, while the concentration remained constant at 0.0150 ± 0.0015 wt. %. The hydrogen concentration increased from 0.0165 ± 0.001 to 0.0370 ± 0.0015 wt. % when the hydrogenation time was extended from 1 to 7 h. The δ-ZrH hydride phase was formed in the Zr layers with Zr crystals reorienting towards the [100] direction. The Nb(110) diffraction reflex shifted towards smaller angles and the interplanar distance in the niobium layers increased, indicating significant lateral compressive stresses. Despite an increase in pressure, the nanohardness and Young’s modulus of the Zr/Nb NMCs remained stable. Increasing the hydrogen concentration to 0.0370 ± 0.0015 wt. % resulted in a 40% increase in nanohardness. At this concentration, the relative values of the Doppler broadening variable energy positron annihilation spectroscopy (S/S0) increased above the initial level, indicating an increase in excess free volume due to hydrogen-induced defects and changes. However, the predominant positron capture center remained intact. The Zr/Nb NMCs with hydrogen content ranging from 0.0150 ± 0.0015 to 0.0180 ± 0.001 wt. % exhibited a decrease in the free volume probed by positrons, as demonstrated by the Doppler broadening variable energy positron annihilation spectroscopy. This was evidenced by opposite changes in S and W (S↓W↑). The microstructural changes are attributed to defect annihilation during hydrogen accumulation near interfaces with the formation of hydrogen–vacancy clusters and hydrides.